cldetect.pcgroup: Search inside pseudospectrum clues for the presence of Cl or...

In yguitton/MeHaloCoA: Fast identification of Cl or Br containing compounds in LC-MS

Description

Fast search of compounds exhibiting chlorinated or brominated pattern (isotopic profile and mass defect) inside a hight-resolution LC-MS data set. After pseudospectrum creation
by CDF2RData or with xcms/CAMERA packages

Usage

cldetect.pcgroup(outdir="",xsAnnotate,pcgroup=c(1:2), plotps=TRUE, deprof=FALSE,
Thresh=30, m1=1.0030, m2=1.997, mdiff=0.05, ppmerr=50, val="into",
 mdiff2=0.001,  myfile="halo_list.csv",myfile2="halo_list_short.csv", m1need=FALSE)

Arguments

outdir	your results directory
xsAnnotate	object of class xsAnnoatet made by CDF2RData or by CAMERA an<-xsannotate
pcgroup	a number or a vector with the pcgroup that should be processed
plotps	Plot pseudospectra and EICs for each considered peaks in jpeg format the result repository default = TRUE. Put FALSE if you have error message like could not find file type (you may have moved your original datas)
deprof	default=FALSE if TRUE deprofile.scan from RMassBank is applied on each pspectra, mainly used if your LC-MS data are not well centroided by your file converter
Thresh	Threshold of intensity for M+2 here 30
m1	mass defect between M and M+1 isotope (here 1.0033)
m2	mass defect between M and M+2 isotope (here 1.997 for Cl)
mdiff	mdiff differences in Da applied to neutral loss search
ppmerr	ppm margin tolerated by cldetect
val	val for use of into or maxo in funM2 and deprofile.scan
mdiff2	mdiff2 differences in Da applied to IFC chromatogram
myfile	name of the output file default "halo_list.csv"
myfile2	name of the output file default "halo_list_short.csv" is a resume from all individual myfile in the case off several files have been processed
m1need	Should M+1 isotope be present? if FALSE (Default) peaks with no M+1 are considered (interesting for low intensity compounds). If TRUE only complete isotopic profiles are taken into account.

Value

A matrix with the Cl or Br peaks annotated.
Draw nice Isotopic Filtered Chromatogram (IFC) summary plot where Cl or Br containings peaks are pointed out on the TIC chromatogram in a PDF file inside the Result directory

Author(s)

Yann GUITTON

References

"Sleno, L., 2012. The use of mass defect in modern mass spectrometry: Mass defect in mass spectrometry. Journal of Mass Spectrometry 47, 226-236. doi:10.1002/jms.2953"
"Wehrens, R., Weingart, G., Mattivi, F., n.d. metaMS: An open-source pipeline for GC-MS-based untargeted metabolomics. Journal of Chromatography B. doi:10.1016/j.jchromb.2014.02.051"

Examples

runGUI()
## Not run:
## Not run: 
library(MeHaloCoA)
data(xcmsSettings) #load peak picking parameters
data(cldetectSettings) #load halogens detection parameters

myfile<-file.path(system.file("doc/mzData", package="MeHaloCoA"),"Q-ToF_Data1.mzData")
an<-CDF2RData(files=myfile, settingslist=xcmsSettings)
result<-cldetect.pcgroup(outdir=getwd(),xsAnnotate=an[[1]],pcgroup=1, plotps=TRUE, deprof=FALSE,
  Thresh=30, m1=1.0030, m2=1.997, mdiff=0.05, ppmerr=50, val="into",
 mdiff2=0.001,  myfile="halo_list.csv",myfile2="halo_list_short.csv", m1need=FALSE)

## End(Not run)

yguitton/MeHaloCoA documentation built on May 3, 2019, 4:30 p.m.